Are you paid, or volunteers? A paid church musician can be fired, but managing volunteers is a whole other kettle of fish. I spent one summer as a replacement for our church's band (unpaid volunteers) and that was enough for me.
As long as you're channeling the energy or whatever it doesn't really matter what the music sounds like.
I've played in a service with a newer drummer who is getting better, but at times has been off beat--which is tricky for a bass player--but he is getting better--although most recently his bass drum was on time, but the ride cymbal was in a different time--threw me off a bit, but I followed his bass drum and tried to tune out the ride cymbal.
The drummer in my band sucks - I am the new guy and I am trying to think of a way to get rid of him. It is actually not that he is a bad player that annoys me per se - the issue is that he seems to be a long time player and he sucks and I doubt he touches his kit between sessions. If he were new, showed potential and practiced a lot, then I probably wouldn't mind.
Why not just tell him? Nicely give him some constructive feedback, along with something that is positive about his playing. Something like "Hey man, you are doing a decent job, especially like the tone of your snare. But I'm having a hard time staying locked in with you because your kick timing is off a lot of the time. Can you work on that?" Don't worry about being too harsh. If someone doesn't tell him, he will continue to torment the ears of you and your other band members.
Take it as an opportunity to help a brother grow in the Lord. Maybe you can help him learn to lock in with you better and before long you guys will be tight as can be!!
Suggest that the band play to a click. That shouldn't be to tough logistically if you are all already wearing in-ear monitors.